Contacts of the helix formed by residues 7 - 14 (chain C) in PDB entry 6P59
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C PRO* 1.3 72.5 - - - +
8C GLN* 1.3 63.2 + - + +
9C ARG 3.3 1.8 - - - -
10C SER* 3.4 19.7 + - - +
11C LYS* 3.6 11.8 + - - +
141C GLN* 4.5 19.8 + - + +
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Residues in contact with GLN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PRO* 3.2 9.4 - - + +
7C ASP* 1.3 78.2 - - + +
9C ARG* 1.3 64.3 + - - +
11C LYS* 3.1 25.3 + - - +
12C PHE* 3.2 10.0 + - - +
105C GLY 3.2 25.0 + - - +
106C VAL* 4.3 11.3 - - + +
107C CYS* 3.7 19.9 - - - +
127C PHE* 3.8 17.4 - - + -
132C ALA* 4.0 25.7 - - - +
140C GLN* 3.3 35.5 + - + +
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Residues in contact with ARG 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PRO* 3.3 42.3 + - - +
8C GLN* 1.3 79.2 - - - +
10C SER* 1.3 68.9 + - - +
12C PHE* 3.3 13.0 + - - +
13C GLU* 3.4 20.0 - - - +
127C PHE* 3.5 29.4 - - + -
129C GLU* 3.7 29.3 - - - +
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Residues in contact with SER 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASP* 3.4 13.8 + - - -
8C GLN 3.2 0.8 - - - -
9C ARG* 1.3 87.3 - - - +
11C LYS* 1.3 61.7 + - - +
13C GLU* 3.1 33.5 + - - +
14C ASN* 3.9 4.3 + - - +
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Residues in contact with LYS 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASP 3.6 6.2 + - - +
8C GLN* 3.1 21.7 + - - +
10C SER* 1.3 76.7 - - - +
12C PHE* 1.3 54.6 + - - +
13C GLU 3.4 0.2 - - - -
14C ASN* 2.5 32.6 - - - +
17C PHE* 3.3 20.2 - - + +
104C ASN* 3.7 17.5 + - + -
105C GLY* 5.4 2.0 - - - -
106C VAL* 4.1 18.9 - - + +
143C PHE* 5.5 0.6 - - - -
144C GLU* 2.8 37.5 + - - +
147C ARG* 4.0 15.0 - - - +
85Z ASN 5.6 1.6 - - - +
87Z SER* 5.9 1.3 - - - +
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Residues in contact with PHE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLN 3.2 10.2 + - - +
9C ARG 3.5 10.5 - - - +
10C SER 3.1 1.2 - - - -
11C LYS* 1.3 76.5 - - - +
13C GLU* 1.3 71.4 + - + +
14C ASN 3.0 10.8 - - - +
17C PHE* 3.8 28.9 - + - -
23C ARG* 3.8 39.3 - - + -
106C VAL* 4.6 3.3 - - + +
108C VAL* 4.2 10.1 - - + -
125C LEU* 3.7 41.5 - - + -
126C GLU* 4.2 11.4 - - - -
127C PHE* 4.1 31.4 - + + -
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG* 3.4 18.9 - - - +
10C SER* 3.1 19.5 + - - +
12C PHE* 1.3 83.0 - - + +
14C ASN* 1.3 62.4 + - - +
15C GLU* 3.3 14.6 - - - +
23C ARG* 3.9 8.6 + - - +
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Residues in contact with ASN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C SER 3.9 4.1 + - - +
11C LYS* 2.5 36.9 + - - +
12C PHE 3.0 13.3 - - - +
13C GLU* 1.3 79.2 - - - +
15C GLU* 1.3 64.2 + - - +
16C GLU 3.8 1.4 + - - -
17C PHE* 3.4 18.3 - - - +
23C ARG* 4.1 3.3 - - - -
85Z ASN* 2.5 35.9 + - + +
86Z SER* 5.0 4.3 - - - -
87Z SER* 4.0 13.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il